Added - ProblemSet6/DNA

Author: BogdanOtava

Week 6 - Python/ProblemSet6/DNA/dna.py

@@ -0,0 +1,92 @@
+"""
+https://cs50.harvard.edu/x/2023/psets/6/dna/
+"""
+
+import csv
+import sys
+
+def main():
+
+ database = []
+ results = {}
+
+ # Check for command-line usage.
+ if len(sys.argv) != 3:
+ print("Usage: python dna.py DATABASE SEQUENCE")
+
+ # Read database file into a variable.
+ with open(sys.argv[1]) as file:
+ reader = csv.reader(file)
+
+ for row in reader:
+ database.append(row)
+
+ # Read DNA sequence file into a variable.
+ with open(sys.argv[2]) as file:
+ sequence = file.read()
+
+ # Find longest match of each STR in DNA sequence.
+ # Get the STRs from the CSV file by iterating through the row starting from 1 so we omit 'name'.
+ for i in range(1, len(database[0])):
+ # Each iteration save the STR in a variable.
+ subsequence = "".join(x for x in database[0][i])
+
+ # In the 'results' dictionary, save each STR along with the length of the longest run.
+ results[subsequence] = longest_match(sequence, subsequence)
+
+ # Convert the results of the STRs to a list containing only the values.
+ sequence_dna = list(results.values())
+
+ # Check database for matching profiles by iterating through the CSV file and getting the STRs for each person.
+ for person in database[1:][0:]:
+ # Save the STR values to a list.
+ person_dna = [int(i) for i in person[1:]]
+
+ # Compare the two lists and print the name of the person if there's a match.
+ if person_dna == sequence_dna:
+ sys.exit(person[0])
+
+ # Print 'No match' if there wasn't a match.
+ print("No match")
+
+
+def longest_match(sequence, subsequence):
+ """Returns length of longest run of subsequence in sequence."""
+
+ # Initialize variables
+ longest_run = 0
+ subsequence_length = len(subsequence)
+ sequence_length = len(sequence)
+
+ # Check each character in sequence for most consecutive runs of subsequence.
+ for i in range(sequence_length):
+
+ # Initialize count of consecutive runs.
+ count = 0
+
+ # Check for a subsequence match in a "substring" (a subset of characters) within sequence.
+ # If a match, move substring to next potential match in sequence.
+ # Continue moving substring and checking for matches until out of consecutive matches.
+ while True:
+
+ # Adjust substring start and end
+ start = i + count * subsequence_length
+ end = start + subsequence_length
+
+ # If there is a match in the substring.
+ if sequence[start:end] == subsequence:
+ count += 1
+
+ # If there is no match in the substring.
+ else:
+ break
+
+ # Update most consecutive matches found.
+ longest_run = max(longest_run, count)
+
+ # After checking for runs at each character in seqeuence, return longest run found.
+ return longest_run
+
+
+if __name__ == "__main__":
+ main()